tbuckley/cabot-search huggingface dataset:
Patient-tailored adoptive immunotherapy with EBV-specific T cells from related and unrelated donors
Authors: Agnes Bonifacius, Britta Lamottke, Sabine Tischer-Zimmermann, Rebecca Schultze-Florey, Lilia Goudeva, Hans-Gert Heuft, Lubomir Arseniev, Rita Beier, Gernot Beutel, Gunnar Cario, Birgit Fröhlich, Johann Greil, Leo Hansmann, Justin Hasenkamp, Michaela Höfs, Patrick Hundsdoerfer, Edgar Jost, Kinan Kafa, Oliver Kriege, Nicolaus Kröger, Stephan Mathas, Roland Meisel, Michaela Nathrath, Mervi Putkonen, Sarina Ravens, Hans Christian Reinhardt, Elisa Sala, Martin G. Sauer, Clemens Schmitt, Roland Schroers, Nina Kristin Steckel, Ralf Ulrich Trappe, Mareike Verbeek, Daniel Wolff, Rainer Blasczyk, Britta Eiz-Vesper, Britta Maecker-Kolhoff
Journal: Journal of Clinical Investigation (2023)

BACKGROUNDAdoptive transfer of EBV-specific T cells can restore specific immunity in immunocompromised patients with EBV-associated complications.METHODSWe provide results of a personalized T cell manufacturing program evaluating donor, patient, T cell product, and outcome data. Patient-tailored clinical-grade EBV-specific cytotoxic T lymphocyte (EBV-CTL) products from stem cell donors (SCDs), related third-party donors (TPDs), or unrelated TPDs from the allogeneic T cell donor registry (alloCELL) at Hannover Medical School were manufactured by immunomagnetic selection using a CliniMACS Plus or Prodigy device and the EBV PepTivators EBNA-1 and Select. Consecutive manufacturing processes were evaluated, and patient outcome and side effects were retrieved by retrospective chart analysis.RESULTSForty clinical-grade EBV-CTL products from SCDs, related TPDs, or unrelated TPDs were generated for 37 patients with refractory EBV infections or EBV-associated malignancies with and without a history of transplantation, within 5 days (median) after donor identification. Thirty-four patients received 1-14 EBV-CTL products (fresh and cryopreserved). EBV-CTL transfer led to a complete response in 20 of 29 patients who were evaluated for clinical response. No infusion-related toxicity was reported. EBV-specific T cells in patients' blood were detectable in 16 of 18 monitored patients (89%) after transfer, and their presence correlated with clinical response.CONCLUSIONPersonalized clinical-grade manufacture of EBV-CTL products via immunomagnetic selection from SCDs, related TPDs, or unrelated TPDs in a timely manner is feasible. Overall, EBV-CTLs were clinically effective and well tolerated. Our data suggest EBV-CTL transfer as a promising therapeutic approach for immunocompromised patients with refractory EBV-associated diseases beyond HSCT, as well as patients with preexisting organ dysfunction.TRIAL REGISTRATIONNot applicable.FUNDINGThis study was funded in part by the German Research Foundation (DFG, 158989968/SFB 900), the Deutsche Kinderkrebsstiftung (DKS 2013.09), Wilhelm-Sander-Stiftung (reference 2015.097.1), Ellen-Schmidt-Program of Hannover Medical School, and German Federal Ministry of Education and Research (reference 01EO0802).
Comparison of Metabolic Response to Colonic Fermentation in Lean Youth vs Youth With Obesity
Authors: Brittany Galuppo, Giuseppina Rosaria Umano, Zhongyao Li, Michelle Van Name, Stephanie L. Samuels, C. Lawrence Kien, Gary W. Cline, David A. Wagner, Emiliano Barbieri, Domenico Tricò, Nicola Santoro
Journal: JAMA Network Open (2023)

Importance Pediatric obesity is a growing health care burden. Understanding how the metabolic phenotype of youth with obesity may modify the effect of intestinal fermentation on human metabolism is key to designing early intervention. Objective To assess whether adiposity and insulin resistance in youth may be associated with colonic fermentation of dietary fibers and its production of acetate, gut-derived hormone secretion, and adipose tissue lipolysis. Design, Setting, and Participants Cross-sectional study of youths aged 15 to 22 years with body mass index in the 25th to 75th percentile or higher than the 85th percentile for age and sex throughout the New Haven County community in Connecticut. Recruitment, studies, and data collection occurred from June 2018 to September 2021. Youths were assigned to a lean, obese insulin sensitive (OIS), or obese insulin resistant (OIR) group. Data were analyzed from April 2022 to September 2022. Exposure Participants consumed 20 g of lactulose during a continuous 10-hour sodium d3-acetate intravenous infusion to measure the rate of appearance of acetate in plasma. Main Outcomes and Measures Plasma was obtained hourly to measure acetate turnover, peptide tyrosine tyrosine (PYY), ghrelin, active glucagon-like peptide 1 (GLP-1), and free fatty acids (FFA). Results A total of 44 youths participated in the study (median [IQR] age, 17.5 [16.0-19.3] years; 25 [56.8%] were female; 23 [52.3%] were White). Consequent to lactulose ingestion, there was a reduction of plasma FFA, an improvement of adipose tissue insulin sensitivity index, an increase in colonic acetate synthesis, and an anorexigenic response characterized by an increased plasma concentration of PYY and active GLP-1 and a reduction of ghrelin in the subgroups. Compared with the lean and OIS groups, the OIR group showed a less marked median (IQR) rate of acetate appearance (OIR: 2.00 [−0.86 to 2.69] μmol × kg −1 × min −1 ; lean: 5.69 [3.04 to 9.77] μmol × kg −1 × min −1 ; lean vs OIR P = .004; OIS: 2.63 [1.22 to 4.52] μmol × kg −1 × min −1 ; OIS vs OIR P = .09), a blunted median (IQR) improvement of adipose insulin sensitivity index (OIR: 0.043 [ 0.006 to 0.155]; lean: 0.277 [0.220 to 0.446]; lean vs OIR P = .002; OIS: 0.340 [0.048 to 0.491]; OIS vs OIR P = .08), and a reduced median (IQR) PYY response (OIR: 25.4 [14.8 to 36.4] pg/mL; lean: 51.3 [31.6 to 83.3] pg/mL; lean vs OIR P = .002; OIS: 54.3 [39.3 to 77.2] pg/mL; OIS vs OIR P = .011). Conclusions and Relevance In this cross-sectional study, lean, OIS, and OIR youth demonstrated different associations between colonic fermentation of indigestible dietary carbohydrates and the metabolic response, with OIR youth showing minimal metabolic modifications as compared with the other 2 groups. Trial Registration ClinicalTrials.gov Identifier: NCT03454828
Codon Optimization Improves the Prediction of Xylose Metabolism from Gene Content in Budding Yeasts
Authors: Rishitha L Nalabothu, Kaitlin J Fisher, Abigail Leavitt LaBella, Taylor A Meyer, Dana A Opulente, John F Wolters, Antonis Rokas, Chris Todd Hittinger
Journal: Molecular Biology and Evolution (2023)

Xylose is the second most abundant monomeric sugar in plant biomass. Consequently, xylose catabolism is an ecologically important trait for saprotrophic organisms, as well as a fundamentally important trait for industries that hope to convert plant mass to renewable fuels and other bioproducts using microbial metabolism. Although common across fungi, xylose catabolism is rare within Saccharomycotina, the subphylum that contains most industrially relevant fermentative yeast species. The genomes of several yeasts unable to consume xylose have been previously reported to contain the full set of genes in the XYL pathway, suggesting the absence of a gene-trait correlation for xylose metabolism. Here, we measured growth on xylose and systematically identified XYL pathway orthologs across the genomes of 332 budding yeast species. Although the XYL pathway coevolved with xylose metabolism, we found that pathway presence only predicted xylose catabolism about half of the time, demonstrating that a complete XYL pathway is necessary, but not sufficient, for xylose catabolism. We also found that XYL1 copy number was positively correlated, after phylogenetic correction, with xylose utilization. We then quantified codon usage bias of XYL genes and found that XYL3 codon optimization was significantly higher, after phylogenetic correction, in species able to consume xylose. Finally, we showed that codon optimization of XYL2 was positively correlated, after phylogenetic correction, with growth rates in xylose medium. We conclude that gene content alone is a weak predictor of xylose metabolism and that using codon optimization enhances the prediction of xylose metabolism from yeast genome sequence data.
One-Year Outcomes Following Intravenous Ketamine Plus Digital Training Among Patients with Treatment-Resistant Depression
Authors: Rebecca B. Price, Meredith L. Wallace, Sanjay J. Mathew, Robert H. Howland
Journal: JAMA Network Open (2023)

This secondary analysis of a randomized clinical trial examines whether automated self-association training can prolong the antidepressant effect of a single infusion of ketamine beyond 1 month in patients with treatment-resistant depression.
Gαi1/3 mediate Netrin-1-CD146-activated signaling and angiogenesis
Authors: Ya Li, Jin-long Chai, Xin Shi, Yu Feng, Jia-jun Li, Li-na Zhou, Cong Cao, Ke-ran Li
Journal: Theranostics (2023)

Netrin-1 binds to the high-affinity receptor CD146 to activate downstream signaling and angiogenesis. Here, we examine the role and underlying mechanisms of G protein subunit alpha i1 (Gαi1) and Gαi3 in Netrin-1-induced signaling and pro-angiogenic activity. In mouse embryonic fibroblasts (MEFs) and endothelial cells, Netrin-1-induced Akt-mTOR (mammalian target of rapamycin) and Erk activation was largely inhibited by silencing or knockout of Gαi1/3, whereas signaling was augmented following Gαi1/3 overexpression. Netrin-1 induced Gαi1/3 association with CD146, required for CD146 internalization, Gab1 (Grb2 associated binding protein 1) recruitment and downstream Akt-mTOR and Erk activation. Netrin-1-induced signaling was inhibited by CD146 silencing, Gab1 knockout, or Gαi1/3 dominant negative mutants. Netrin-1-induced human umbilical vein endothelial cell (HUVEC) proliferation, migration and tube formation were inhibited by Gαi1/3 short hairpin RNA (shRNA), but were potentiated by ectopic Gαi1/3 overexpression. In vivo, intravitreous injection of Netrin-1 shRNA adeno-associated virus (AAV) significantly inhibited Akt-mTOR and Erk activation in murine retinal tissues and reduced retinal angiogenesis. Endothelial knockdown of Gαi1/3 significantly inhibited Netrin1-induced signaling and retinal angiogenesis in mice. Netrin-1 mRNA and protein expression were significantly elevated in retinal tissues of diabetic retinopathy (DR) mice. Importantly, silence of Netrin-1, by intravitreous Netrin-1 shRNA AAV injection, inhibited Akt-Erk activation, pathological retinal angiogenesis and retinal ganglion cells degeneration in DR mice. Lastly, Netrin-1 and CD146 expression is significantly increased in the proliferative retinal tissues of human proliferative diabetic retinopathy patients. Together, Netrin-1 induces CD146-Gαi1/3-Gab1 complex formation to mediate downstream Akt-mTOR and Erk activation, important for angiogenesis in vitro and in vivo.
SARS-CoV-2 Testing and Complications Across 6 Waves of the COVID-19 Pandemic Among Individuals Recently Experiencing Homelessness in Ontario, Canada
Authors: Salimah Z. Shariff, Jennifer N. Reid, Andrew S. Boozary, Richard Booth
Journal: JAMA Network Open (2023)

This cohort study compares the rates of SARS-CoV-2 testing and complications across 6 waves of the COVID-19 pandemic in Ontario, Canada, between individuals recently experiencing homelessness, low-income residents, and the general population.
Changes in Minoxidil Prescribing After Media Attention About Oral Use for Hair Loss
Authors: Brianna M. Goodwin Cartwright, Michael Wang, Patricia Rodriguez, Sarah Stewart, Christopher M. Worsham, Nick Stucky, Anupam B. Jena
Journal: JAMA Network Open (2023)

This cross-sectional study investigates rates of prescription of low-dose minoxidil after of publication of a newspaper article on this treatment.
IL11 signaling mediates piR-2158 suppression of cell stemness and angiogenesis in breast cancer
Authors: Qian Zhao, Lu Qian, Yuefan Guo, Jinhui Lü, Danni Li, Heying Xie, Qiong Wang, Wenjing Ma, Pengfei Liu, Yu Liu, Tao Wang, Xuebiao Wu, Junyi Han, Zuoren Yu
Journal: Theranostics (2023)

Emerging evidence has indicated the aberrant expression of PIWI-interacting RNAs (piRNAs) in human cancer cells to regulate tumor development and progression by governing cancer cell stemness.Herein, we identified downregulation of piR-2158 in human breast cancer tumors, especially in ALDH+ breast cancer stem cells (BCSCs) from patients and cell lines, which was further validated in two types of genetically engineered mouse models of breast cancer (MMTV-Wnt and MMTV-PyMT).Enforced overexpression of piR-2158 in basal-like or luminal subtypes of breast cancer cells suppressed cell proliferation, migration, epithelial-mesenchymal transition (EMT) and stemness in vitro.Administration of a dual mammary tumor-targeting piRNA delivery system in mice reduced tumor growth in vivo.RNA-seq, ChIP-seq and luciferase reporter assays demonstrated piR-2158 as a transcriptional repressor of IL11 by competing with AP-1 transcription factor subunit FOSL1 to bind the promoter of IL11.STAT3 signaling mediated piR-2158-IL11 regulation of cancer cell stemness and tumor growth.Moreover, by co-culturing of MDA-MB-231 and HUVECs in vitro and CD31 staining of tumor endothelial cells in vivo, we demonstrated inhibition of angiogenesis by piR-2158-IL11 in breast cancer.In conclusion, the current study not only reveals a novel mechanism through which piR-2158 inhibits mammary gland tumorigenesis via regulating cancer stem cells and tumor angiogenesis, but also provides a novel therapeutic strategy in treatment of breast cancer.
Single‐cell atlas reveals a distinct immune profile fostered by T cell‐B cell crosstalk in triple negative breast cancer
Authors: Shuning Ding, Niu Qiao, Qingchen Zhu, Yiwei Tong, Shengyue Wang, Xiaosong Chen, Qiang Tian, Yichuan Xiao, Kunwei Shen
Journal: Cancer Communications (2023)

Abstract Background Characterizing the unique immune microenvironment of each tumor is of great importance for better predicting prognosis and guiding cancer immunotherapy. However, the unique features of the immune microenvironment of triple negative breast cancer (TNBC) compared with other subtypes of breast cancer remain elusive. Therefore, we aimed to depict and compare the immune landscape among TNBC, human epidermal growth factor receptor 2‐positive (HER2 + ) breast cancer, and luminal‐like breast cancer. Methods Single‐cell RNA sequencing (scRNA‐seq) was performed on CD45 + immune cells isolated from human normal breast tissues and primary breast tumors of various subtypes. By analyzing the scRNA‐seq data, immune cell clusters were identified and their proportions as well as transcriptome features were compared among TNBC, human HER2 + breast cancer, and luminal‐like breast cancer. Pseudotime and cell‐cell communication analyses were also conducted to characterize the immune microenvironment. Results ScRNA‐seq data of 117,958 immune cells were obtained and 31 immune clusters were identified. A unique immunosuppressive microenvironment in TNBC was decoded as compared to that in HER2 + or luminal‐like breast cancer, which was characterized by higher proportions of regulatory T cells (Tregs) and exhausted CD8 + T cells and accompanied by more abundant plasma cells. Tregs and exhausted CD8 + T cells in TNBC exhibited increased immunosuppression signature and dysfunctional scores. Pseudotime analyses showed that B cells tended to differentiate to plasma cells in TNBC. Cell‐cell communication analyses indicated that these unique features are fostered by the diversified T cell‐B cell crosstalk in TNBC. Based on the T cell‐B cell crosstalk, a prognostic signature was established that could effectively predict the prognosis status for patients with TNBC. Additionally, it was found that TNBC had a higher proportion of cytotoxic natural killer (NK) cells, whereas HER2 + or luminal‐like breast cancer lost this feature, suggesting that HER2 + or luminal‐like breast cancer, but not TNBC, may benefit from NK‐based immunotherapy. Conclusions This study identified a distinct immune feature fostered by T cell‐B cell crosstalk in TNBC, which provides better prognostic information and effective therapeutic targets for breast cancer.
SaaS sRNA promotes <i>Salmonella</i> intestinal invasion via modulating MAPK inflammatory pathway
Authors: Linlin Cai, Yunting Xie, Liangting Shao, Haijing Hu, Xinglian Xu, Huhu Wang, Guanghong Zhou
Journal: Gut Microbes (2023)

Salmonella Enteritidis is a foodborne enteric pathogen that infects humans and animals, utilizing complex survival strategies. Bacterial small RNA (sRNA) plays an important role in these strategies. However, the virulence regulatory network of S. Enteritidis remains largely incomplete and knowledge of gut virulence mechanisms of sRNAs is limited. Here, we characterized the function of a previously identified Salmonella adhesive-associated sRNA (SaaS) in the intestinal pathogenesis of S. Enteritidis. We found that SaaS promoted bacterial colonization in both cecum and colon of a BALB/c mouse model; it was preferentially expressed in colon. Moreover, our results showed that SaaS enhanced damage to mucosal barrier by affecting expressions of antimicrobial products, decreasing the number of goblet cells, suppressing mucin gene expression, and eventually reducing thickness of mucus layer; it further breached below physical barrier by strengthening invasion into epithelial cells in Caco-2 cell model as well as decreasing tight junction expressions. High throughput 16S rRNA gene sequencing revealed that SaaS also altered gut homeostasis by depleting beneficial gut microbiota while increasing harmful ones. Furthermore, by employing ELISA and western blot analysis, we demonstrated that SaaS regulated intestinal inflammation through sequential activation P38-JNK-ERK MAPK signaling pathway, which enabled immune escape at primary infection stage but strengthened pathogenesis at later stage, respectively. These findings suggest that SaaS plays an essential role in the virulence of S. Enteritidis and reveals its biological role in intestinal pathogenesis.
Aldehyde dehydrogenase 1A1 confers erlotinib resistance via facilitating the reactive oxygen species-reactive carbonyl species metabolic pathway in lung adenocarcinomas: Erratum
Authors: Hui-Min Lei, Ke-Ren Zhang, Cong Hui Wang, Yang Wang, Guang-Lei Zhuang, Li-Ming Lu, Jian Zhang, Ying Shen, Hong-Zhuan Chen, Liang Zhu
Journal: Theranostics (2023)

[This corrects the article DOI: 10.7150/thno.35729.].
Dynamics of Gene Loss following Ancient Whole-Genome Duplication in the Cryptic<i>Paramecium</i>Complex
Authors: Jean-Francois Gout, Yue Hao, Parul Johri, Olivier Arnaiz, Thomas G Doak, Simran Bhullar, Arnaud Couloux, Fréderic Guérin, Sophie Malinsky, Alexey Potekhin, Natalia Sawka, Linda Sperling, Karine Labadie, Eric Meyer, Sandra Duharcourt, Michael Lynch
Journal: Molecular Biology and Evolution (2023)

Abstract Whole-genome duplications (WGDs) have shaped the gene repertoire of many eukaryotic lineages. The redundancy created by WGDs typically results in a phase of massive gene loss. However, some WGD–derived paralogs are maintained over long evolutionary periods, and the relative contributions of different selective pressures to their maintenance are still debated. Previous studies have revealed a history of three successive WGDs in the lineage of the ciliate Paramecium tetraurelia and two of its sister species from the Paramecium aurelia complex. Here, we report the genome sequence and analysis of 10 additional P. aurelia species and 1 additional out group, revealing aspects of post-WGD evolution in 13 species sharing a common ancestral WGD. Contrary to the morphological radiation of vertebrates that putatively followed two WGD events, members of the cryptic P. aurelia complex have remained morphologically indistinguishable after hundreds of millions of years. Biases in gene retention compatible with dosage constraints appear to play a major role opposing post-WGD gene loss across all 13 species. In addition, post-WGD gene loss has been slower in Paramecium than in other species having experienced genome duplication, suggesting that the selective pressures against post-WGD gene loss are especially strong in Paramecium. A near complete lack of recent single-gene duplications in Paramecium provides additional evidence for strong selective pressures against gene dosage changes. This exceptional data set of 13 species sharing an ancestral WGD and 2 closely related out group species will be a useful resource for future studies on Paramecium as a major model organism in the evolutionary cell biology.
Impact of fatty liver on long-term outcomes in chronic hepatitis B: a systematic review and matched analysis of individual patient data meta-analysis
Authors: Yu Jun Wong, Vy H. Nguyen, Hwai-I Yang, Jie Li, Michael Huan Le, Wan-Jung Wu, Nicole Xinrong Han, Khi Yung Fong, Elizebeth Chen, Connie Wong, Fajuan Rui, Xiaoming Xu, Qi Xue, Xin Yu Hu, Wei Qiang Leow, George Boon-Bee Goh, Ramsey Cheung, Grace Wong, Vincent Wai-Sun Wong, Ming-Whei Yu, Mindie H. Nguyen
Journal: Clinical and Molecular Hepatology (2023)

Background/Aims: Chronic hepatitis B (CHB) and fatty liver (FL) often co-exist, but natural history data of this dual condition (CHB-FL) are sparse. Via a systematic review, conventional meta-analysis (MA) and individual patient-level data MA (IPDMA), we compared liver-related outcomes and mortality between CHB-FL and CHB-no FL patients.Methods: We searched 4 databases from inception to December 2021 and pooled study-level estimates using a random- effects model for conventional MA. For IPDMA, we evaluated outcomes after balancing the two study groups with inverse probability treatment weighting (IPTW) on age, sex, cirrhosis, diabetes, ALT, HBeAg, HBV DNA, and antiviral treatment.Results: We screened 2,157 articles and included 19 eligible studies (17,955 patients: 11,908 CHB-no FL; 6,047 CHB-FL) in conventional MA, which found severe heterogeneity (I2=88–95%) and no significant differences in HCC, cirrhosis, mortality, or HBsAg seroclearance incidence (P=0.27–0.93). IPDMA included 13,262 patients: 8,625 CHB-no FL and 4,637 CHB-FL patients who differed in several characteristics. The IPTW cohort included 6,955 CHB-no FL and 3,346 CHB-FL well-matched patients. CHB-FL patients (vs. CHB-no FL) had significantly lower HCC, cirrhosis, mortality and higher HBsAg seroclearance incidence (all p≤0.002), with consistent results in subgroups. CHB-FL diagnosed by liver biopsy had a higher 10-year cumulative HCC incidence than CHB-FL diagnosed with non-invasive methods (63.6% vs. 4.3%, p&lt;0.0001).Conclusions: IPDMA data with well-matched CHB patient groups showed that FL (vs. no FL) was associated with significantly lower HCC, cirrhosis, and mortality risk and higher HBsAg seroclearance probability.